null Mon 24 Dec 07:26:24 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2iiu-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2iiu-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2iiu-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:26:28 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 487 and 0 Target number of residues in the AU: 487 Target solvent content: 0.6546 Checking the provided sequence file Detected sequence length: 227 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 681 Adjusted target solvent content: 0.52 Input MTZ file: 2iiu-4.0-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 155 Cell parameters: 99.900 99.900 397.311 90.000 90.000 120.000 Input sequence file: 2iiu-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 5448 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 132.437 4.000 Wilson plot Bfac: 80.80 6724 reflections ( 98.74 % complete ) and 0 restraints for refining 5999 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3775 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3272 (Rfree = 0.000) for 5999 atoms. Found 16 (28 requested) and removed 56 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 6049 seeds are put forward NCS extension: 0 residues added, 6049 seeds are put forward Round 1: 134 peptides, 27 chains. Longest chain 11 peptides. Score 0.248 Round 2: 183 peptides, 36 chains. Longest chain 9 peptides. Score 0.275 Round 3: 205 peptides, 39 chains. Longest chain 13 peptides. Score 0.298 Round 4: 226 peptides, 40 chains. Longest chain 13 peptides. Score 0.338 Round 5: 227 peptides, 39 chains. Longest chain 10 peptides. Score 0.350 Taking the results from Round 5 Chains 39, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12389 restraints for refining 4919 atoms. 11676 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2884 (Rfree = 0.000) for 4919 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 2: After refmac, R = 0.2722 (Rfree = 0.000) for 4868 atoms. Found 14 (23 requested) and removed 31 (11 requested) atoms. Cycle 3: After refmac, R = 0.2624 (Rfree = 0.000) for 4827 atoms. Found 6 (23 requested) and removed 14 (11 requested) atoms. Cycle 4: After refmac, R = 0.2590 (Rfree = 0.000) for 4810 atoms. Found 5 (22 requested) and removed 14 (11 requested) atoms. Cycle 5: After refmac, R = 0.2483 (Rfree = 0.000) for 4793 atoms. Found 7 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 4931 seeds are put forward NCS extension: 0 residues added, 4931 seeds are put forward Round 1: 175 peptides, 37 chains. Longest chain 9 peptides. Score 0.243 Round 2: 237 peptides, 44 chains. Longest chain 14 peptides. Score 0.323 Round 3: 228 peptides, 41 chains. Longest chain 10 peptides. Score 0.332 Round 4: 230 peptides, 40 chains. Longest chain 11 peptides. Score 0.347 Round 5: 224 peptides, 38 chains. Longest chain 10 peptides. Score 0.354 Taking the results from Round 5 Chains 38, Residues 186, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12031 restraints for refining 4841 atoms. 11300 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2837 (Rfree = 0.000) for 4841 atoms. Found 14 (23 requested) and removed 28 (11 requested) atoms. Cycle 7: After refmac, R = 0.2617 (Rfree = 0.000) for 4819 atoms. Found 6 (22 requested) and removed 15 (11 requested) atoms. Cycle 8: After refmac, R = 0.2586 (Rfree = 0.000) for 4808 atoms. Found 2 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.2543 (Rfree = 0.000) for 4788 atoms. Found 3 (22 requested) and removed 15 (11 requested) atoms. Cycle 10: After refmac, R = 0.2634 (Rfree = 0.000) for 4771 atoms. Found 9 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 4927 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 4936 seeds are put forward Round 1: 198 peptides, 40 chains. Longest chain 8 peptides. Score 0.270 Round 2: 239 peptides, 44 chains. Longest chain 12 peptides. Score 0.328 Round 3: 237 peptides, 42 chains. Longest chain 13 peptides. Score 0.343 Round 4: 243 peptides, 44 chains. Longest chain 9 peptides. Score 0.337 Round 5: 249 peptides, 42 chains. Longest chain 11 peptides. Score 0.370 Taking the results from Round 5 Chains 42, Residues 207, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12234 restraints for refining 4919 atoms. 11448 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2861 (Rfree = 0.000) for 4919 atoms. Found 23 (23 requested) and removed 18 (11 requested) atoms. Cycle 12: After refmac, R = 0.2769 (Rfree = 0.000) for 4920 atoms. Found 8 (23 requested) and removed 13 (11 requested) atoms. Cycle 13: After refmac, R = 0.2730 (Rfree = 0.000) for 4914 atoms. Found 5 (23 requested) and removed 14 (11 requested) atoms. Cycle 14: After refmac, R = 0.2697 (Rfree = 0.000) for 4903 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.2680 (Rfree = 0.000) for 4887 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 5023 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 5034 seeds are put forward Round 1: 212 peptides, 43 chains. Longest chain 8 peptides. Score 0.273 Round 2: 249 peptides, 44 chains. Longest chain 12 peptides. Score 0.351 Round 3: 246 peptides, 42 chains. Longest chain 12 peptides. Score 0.364 Round 4: 236 peptides, 42 chains. Longest chain 13 peptides. Score 0.341 Round 5: 237 peptides, 40 chains. Longest chain 10 peptides. Score 0.363 Taking the results from Round 3 Chains 42, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12086 restraints for refining 4920 atoms. 11312 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2838 (Rfree = 0.000) for 4920 atoms. Found 21 (23 requested) and removed 12 (11 requested) atoms. Cycle 17: After refmac, R = 0.2716 (Rfree = 0.000) for 4922 atoms. Found 1 (23 requested) and removed 15 (11 requested) atoms. Cycle 18: After refmac, R = 0.2689 (Rfree = 0.000) for 4907 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 19: After refmac, R = 0.2659 (Rfree = 0.000) for 4895 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.2648 (Rfree = 0.000) for 4883 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 5044 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5059 seeds are put forward Round 1: 223 peptides, 47 chains. Longest chain 8 peptides. Score 0.258 Round 2: 249 peptides, 45 chains. Longest chain 9 peptides. Score 0.341 Round 3: 234 peptides, 43 chains. Longest chain 11 peptides. Score 0.326 Round 4: 242 peptides, 43 chains. Longest chain 10 peptides. Score 0.345 Round 5: 248 peptides, 43 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 5 Chains 43, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12185 restraints for refining 4919 atoms. 11408 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2917 (Rfree = 0.000) for 4919 atoms. Found 17 (23 requested) and removed 18 (11 requested) atoms. Cycle 22: After refmac, R = 0.2716 (Rfree = 0.000) for 4909 atoms. Found 6 (23 requested) and removed 18 (11 requested) atoms. Cycle 23: After refmac, R = 0.2672 (Rfree = 0.000) for 4889 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 24: After refmac, R = 0.2649 (Rfree = 0.000) for 4879 atoms. Found 1 (23 requested) and removed 16 (11 requested) atoms. Cycle 25: After refmac, R = 0.2644 (Rfree = 0.000) for 4864 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 5007 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5019 seeds are put forward Round 1: 207 peptides, 42 chains. Longest chain 11 peptides. Score 0.271 Round 2: 229 peptides, 42 chains. Longest chain 16 peptides. Score 0.325 Round 3: 227 peptides, 36 chains. Longest chain 20 peptides. Score 0.381 Round 4: 227 peptides, 40 chains. Longest chain 15 peptides. Score 0.340 Round 5: 230 peptides, 36 chains. Longest chain 20 peptides. Score 0.387 Taking the results from Round 5 Chains 36, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12372 restraints for refining 4919 atoms. 11632 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2999 (Rfree = 0.000) for 4919 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. Cycle 27: After refmac, R = 0.2880 (Rfree = 0.000) for 4927 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 28: After refmac, R = 0.2842 (Rfree = 0.000) for 4922 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.2817 (Rfree = 0.000) for 4913 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2805 (Rfree = 0.000) for 4901 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 5043 seeds are put forward NCS extension: 33 residues added (5 deleted due to clashes), 5076 seeds are put forward Round 1: 214 peptides, 45 chains. Longest chain 11 peptides. Score 0.257 Round 2: 214 peptides, 39 chains. Longest chain 16 peptides. Score 0.320 Round 3: 206 peptides, 35 chains. Longest chain 13 peptides. Score 0.343 Round 4: 205 peptides, 36 chains. Longest chain 11 peptides. Score 0.330 Round 5: 211 peptides, 37 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 3 Chains 35, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12391 restraints for refining 4919 atoms. 11742 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2866 (Rfree = 0.000) for 4919 atoms. Found 16 (23 requested) and removed 11 (11 requested) atoms. Cycle 32: After refmac, R = 0.2714 (Rfree = 0.000) for 4919 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.2709 (Rfree = 0.000) for 4906 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.2697 (Rfree = 0.000) for 4898 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.2667 (Rfree = 0.000) for 4889 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 5013 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 5027 seeds are put forward Round 1: 189 peptides, 40 chains. Longest chain 10 peptides. Score 0.247 Round 2: 218 peptides, 40 chains. Longest chain 12 peptides. Score 0.319 Round 3: 211 peptides, 36 chains. Longest chain 13 peptides. Score 0.344 Round 4: 207 peptides, 38 chains. Longest chain 12 peptides. Score 0.313 Round 5: 205 peptides, 35 chains. Longest chain 13 peptides. Score 0.340 Taking the results from Round 3 Chains 36, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12223 restraints for refining 4918 atoms. 11559 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2879 (Rfree = 0.000) for 4918 atoms. Found 23 (23 requested) and removed 12 (11 requested) atoms. Cycle 37: After refmac, R = 0.2754 (Rfree = 0.000) for 4925 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.2731 (Rfree = 0.000) for 4920 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.2671 (Rfree = 0.000) for 4911 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.2679 (Rfree = 0.000) for 4902 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 5014 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5029 seeds are put forward Round 1: 197 peptides, 43 chains. Longest chain 9 peptides. Score 0.235 Round 2: 220 peptides, 40 chains. Longest chain 13 peptides. Score 0.324 Round 3: 210 peptides, 37 chains. Longest chain 13 peptides. Score 0.331 Round 4: 210 peptides, 37 chains. Longest chain 13 peptides. Score 0.331 Round 5: 202 peptides, 35 chains. Longest chain 13 peptides. Score 0.333 Taking the results from Round 5 Chains 35, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12476 restraints for refining 4919 atoms. 11843 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2919 (Rfree = 0.000) for 4919 atoms. Found 17 (23 requested) and removed 11 (11 requested) atoms. Cycle 42: After refmac, R = 0.2749 (Rfree = 0.000) for 4924 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.2748 (Rfree = 0.000) for 4914 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.2745 (Rfree = 0.000) for 4905 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.2717 (Rfree = 0.000) for 4896 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 5015 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5033 seeds are put forward Round 1: 163 peptides, 35 chains. Longest chain 7 peptides. Score 0.233 Round 2: 176 peptides, 32 chains. Longest chain 14 peptides. Score 0.302 Round 3: 193 peptides, 35 chains. Longest chain 13 peptides. Score 0.311 Round 4: 195 peptides, 32 chains. Longest chain 11 peptides. Score 0.348 Round 5: 189 peptides, 32 chains. Longest chain 11 peptides. Score 0.334 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2iiu-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6724 reflections ( 98.74 % complete ) and 12573 restraints for refining 4920 atoms. 11953 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2994 (Rfree = 0.000) for 4920 atoms. Found 0 (23 requested) and removed 10 (11 requested) atoms. Cycle 47: After refmac, R = 0.2897 (Rfree = 0.000) for 4910 atoms. Found 0 (23 requested) and removed 5 (11 requested) atoms. Cycle 48: After refmac, R = 0.2854 (Rfree = 0.000) for 4905 atoms. Found 0 (23 requested) and removed 4 (11 requested) atoms. Cycle 49: After refmac, R = 0.2835 (Rfree = 0.000) for 4901 atoms. Found 0 (23 requested) and removed 2 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:20:12 GMT 2018 Job finished. TimeTaking 53.8 Used memory is bytes: 6232456